Similar protocols

Pipeline publication

[…] -layout-consensus assembler developed and used to reconstruct the first genome sequence of a multicellular organism, D. melanogaster , as well as one of the first diploid human genome sequences . Our Celera-generated assembly contained 6,617 contigs of lengths ranging from 1,506 bp to 567.5 Kbp, with an N50 contig length of 64.1 Kbp. Note that because the TruSeq synthetic long-read data are effectively single-end reads, only contig rather than scaffold metrics are reported. The total length of the assembly (i.e. the sum of all contig lengths) was 152.2 Mbp, with a GC content of 42.18% (compared to 41.74% GC content in the reference genome). Upon aligning contigs to the reference genome with NUCmer , , we observed that the ends of several contigs overlapped with long stretches (1 Kbp) of perfect sequence identity. We therefore used the assembly program Minimus2 to merge across these regions to generate supercontigs. All statistics in the following sections are based on this two-step assembly procedure combining Celera and Minimus2. The merging step resulted in the additional merging of 1,652 input contigs into 633 supercontigs, resulting in an improved assembly with a total of 5,598 contigs spanning a total of 147.4 Mbp and an N50 contig length of 69.7 Kbp ()., The N50 length metric measures the length of the contig for which 50% of the total assembly length is contained in contigs of that size or larger, while the L50 metric is the rank order of that contig if all contigs are ordered from longest to shortest. NG50 and LG50 are similar, but based on the expected genome size of 180 Mbp rather than the assembly length. QUAST metrics are based on alignment of contigs to the euchromatic reference chromosome arms (which also contain most of the centric heterochromatin). NA50 and LA50 are analogous to N50 and L50, respectively, but in this case the lengths of aligned blocks rather than contigs are considered., Values in parentheses represent metrics calculated upon inclusion of the heterochromatic reference scaffolds (XHet, 2LHet, 2RHet, 3LHet, 3RHet, YHet, and U), which contain gaps of arbitrary size and are in some cases not oriented with respect to one another . Values outside of parentheses represent comparison of the assembly only to high-quality reference scaffolds X, 2L, 2R, 3L, 3R, and 4., We used the […]

Pipeline specifications

Software tools SGA, BLASTN, BWA, GATK, JVARKIT
Organisms Drosophila melanogaster